It should be noted that the real reason why characters can travel through the Multiverse is because Nitori invented a beaming system that can teleport you to any planet or dimension at any point in the universe.

It's the same technology that would later be used in the "Star Trek" portion of the future (as seen in "Star Trek Into Darkness").

It should be noted that Trixie is part of the Angry Joe Army and, as such, knows aboutr the parallel universe and dimension in the Multiverse, but she doesn't travel to them often in order not to break The Oath.

i predict that the alternate ending will Twilight will stay in the human world because either Sunset Shimmer destroys the portal, or the part after Twilight is about to say goodbye to her human friends and decides to actually stay.